GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gnl in Amantichitinum ursilacus IGB-41

Align gluconolactonase (EC 3.1.1.17) (characterized)
to candidate WP_053939460.1 WG78_RS19225 SMP-30/gluconolactonase/LRE family protein

Query= BRENDA::Q64374
         (299 letters)



>NCBI__GCF_001294205.1:WP_053939460.1
          Length = 301

 Score =  106 bits (264), Expect = 7e-28
 Identities = 78/266 (29%), Positives = 124/266 (46%), Gaps = 26/266 (9%)

Query: 35  PSKIICRWDTVSNQVQRVAVDAPVSSVALRQLGGYVATIGTKFCALNWENQSVFVLAMVD 94
           P ++ C   T  + V  VA DA ++                     N  + ++  L  V+
Sbjct: 59  PQRVCCFAFTQDDDVLLVAFDAGLA-------------------LFNTASGAIKRLTPVE 99

Query: 95  EDKKNNRFNDGKVDPAGRYFAGTMAEETAPAVLERHQGSLYSLFPDHSVKKY-FDQVDIS 153
            +    R NDG+VD AG    GTM E +A A     +G  Y    +  +++     + IS
Sbjct: 100 PETPGTRCNDGRVDRAGNLVFGTMHERSAEA-----KGHFYRFDTESRLQQLALPAIAIS 154

Query: 154 NGLDWSLDHKIFYYIDSLSYTVDAFDYDLQTGQISNRRIVYKMEKDEQIPDGMCIDAEGK 213
           N L +S D    Y+ DSL + +    YD  TG I+   + + +      PDG  +DA G 
Sbjct: 155 NSLAFSPDGGTLYWCDSLQHKIMQCAYDSVTGAIAEISVFHDLGDTVIEPDGSTVDAAGY 214

Query: 214 LWVACYNGGRVIRLDPETGKRLQTVKLPVDKTTSCCFGGKDYSEMYVTCARDGLNAEGLL 273
           LW A + G  V R  P+ G   + + LPV + T   FGG + + +++T AR GL+   L 
Sbjct: 215 LWNAEWAGHCVTRYAPD-GSIDRKIHLPVAQPTCVTFGGPEQNTLFITSARAGLDDAALA 273

Query: 274 RQPDAGNIFKITGLGVKGIAPYSYAG 299
           +QP+AG++F +   GV+G+    + G
Sbjct: 274 QQPEAGSVFALEIPGVRGLPENIWLG 299


Lambda     K      H
   0.319    0.137    0.419 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 260
Number of extensions: 17
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 299
Length of database: 301
Length adjustment: 27
Effective length of query: 272
Effective length of database: 274
Effective search space:    74528
Effective search space used:    74528
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory